1. Good - now make sure that the log files are getting written to that archivedlogs folder. Specifically, look to see that the Scheduler > Trace > TaskExecution log files are getting written there.
You can also remove all the "governance" QVDs created in programdata\qlik\sense\log. And then try the reloads again.
2.Are you getting an error when reloading -- namely an error saying you can't connect to the REST data connection or QVXConnect error of some sort?
You can open the Ops Mon app and check the Apps page to see if there is data there. Or, you can check the License Monitor app dashboard/overview page and see if you have a count of total tokens KPI working.
3. the Qlik Sense Repository database --- this is a live database, so there is not so much a notion of "history". You need the QSR database running in order to use Qlik Sense, so it is not removing "history". Is there a specific piece of information you are concerned about?
4. I think if you make sure your data connections are correct per the documentation, and you remove the existing "governance" QVDs and then reload the apps, you should see your history. If not, I would guess that the log files are either missing (deleted) or are stored in a different location.